We will learn computational methods -- algorithms and data structures -- for analyzing DNA sequencing data. We will learn a little about DNA, genomics, and how DNA sequencing is used. We will use Python to implement key algorithms and data structures and to analyze real genomes and DNA sequencing datasets.

Taught By

Ben Langmead, PhD

Assistant Professor

Jacob Pritt

Transcript

In this practical we'll extend the overlap function that we wrote in the last practical, and use it to create a naive overlap map for a set of reads. So I've already pasted in here the function that we wrote that calculates the overlap between two strings a and b. Another function we're going to use here is permutations, which is in Python so I'm going to start by saying from itertools import permutations. And now just to give you an example of what this does, I'm going to print out permutations. I'm going to give it a list. I'll just give it 1, 2, and 3, and I'm going to give it the length of the permutations that I want. So I'll start by just saying 1. And so this prints out all the permutations of this set of size 1. So in this case they can be 1, 2, or 3. I can get all the permutations of size 2, and this will get me all of the pairs, which are ordered. And similarly, I can do all the permutations of size 3, and this gives me all the size 3 permutations of that list. So now let's write our function naive_overlap. We'll take a set of reads and a minimum overlap y of k. And so I'm going to store my overlap map as a dictionary. And now what I'm going to do is I'm going to say for each pair of reads a, b, in permutations of reads, 2. So I'll get all the pairs of reads in that set. And I'm going to calculate the overlap length using the function above. And all I'm going to do is I'm going to say, if that length is greater than zero, then, add the tuple a, b to the dictionary as a key and give it a value of that overlap length. And I'll just return overlaps. So now let's do this for a simple set of reads. Give it a minimum length of 3 and let me try to get something that will work There we go. So there's an example of, so in this case, the first two reads overlap. First read overlaps the second one, and the third read overlaps the first one.

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